Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 16 of 320
Found at i:4394743 original size:18 final size:17
Alignment explanation
Indices: 4394716--4394750 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4394706 TTGTATAGGT
4394716 GGGATTTTTTTTAATAC
1 GGGATTTTTTTTAATAC
4394733 GGGATTTTTTTTAATAC
1 GGGATTTTTTTTAATAC
4394750 G
1 G
4394751 AACACATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (17 bp):
GGGATTTTTTTTAATAC
Found at i:4397576 original size:27 final size:27
Alignment explanation
Indices: 4397543--4397652 Score: 179
Period size: 27 Copynumber: 4.1 Consensus size: 27
4397533 TAAAAACGTC
4397543 ATATTCTCCATTAAAGTAAATAGTAAA
1 ATATTCTCCATTAAAGTAAATAGTAAA
*
4397570 ATATTCTCCATTAAAGTAAATAACGT--C
1 ATATTCTCCATTAAAGTAAAT-A-GTAAA
4397597 ATATTCTCCATTAAAGTAAATAGTAAA
1 ATATTCTCCATTAAAGTAAATAGTAAA
4397624 ATATTCTCCATTAAAGTAAATAGTAAA
1 ATATTCTCCATTAAAGTAAATAGTAAA
4397651 AT
1 AT
4397653 CATCTTTTCT
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
25 2 0.03
26 1 0.01
27 71 0.92
28 1 0.01
29 2 0.03
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (27 bp):
ATATTCTCCATTAAAGTAAATAGTAAA
Found at i:4397599 original size:54 final size:54
Alignment explanation
Indices: 4397530--4397645 Score: 225
Period size: 54 Copynumber: 2.2 Consensus size: 54
4397520 AAACTTATAT
4397530 AAGTAAA-AACGTCATATTCTCCATTAAAGTAAATAGTAAAATATTCTCCATTA
1 AAGTAAATAACGTCATATTCTCCATTAAAGTAAATAGTAAAATATTCTCCATTA
4397583 AAGTAAATAACGTCATATTCTCCATTAAAGTAAATAGTAAAATATTCTCCATTA
1 AAGTAAATAACGTCATATTCTCCATTAAAGTAAATAGTAAAATATTCTCCATTA
4397637 AAGTAAATA
1 AAGTAAATA
4397646 GTAAAATCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 7 0.11
54 55 0.89
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (54 bp):
AAGTAAATAACGTCATATTCTCCATTAAAGTAAATAGTAAAATATTCTCCATTA
Found at i:4401068 original size:15 final size:17
Alignment explanation
Indices: 4401039--4401079 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
4401029 GTACAATGGC
4401039 ATCAA-TCATGCAATAT
1 ATCAATTCATGCAATAT
4401055 -TCAATTCATG-AATAT
1 ATCAATTCATGCAATAT
*
4401070 ATCATTTCAT
1 ATCAATTCAT
4401080 ACCATACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (17 bp):
ATCAATTCATGCAATAT
Found at i:4401862 original size:13 final size:14
Alignment explanation
Indices: 4401836--4401868 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
4401826 ATTTTCTCCA
4401836 TTCTTTTTCTTTCT
1 TTCTTTTTCTTTCT
4401850 TTCTTTTTC-TTCT
1 TTCTTTTTCTTTCT
4401863 TTCTTT
1 TTCTTT
4401869 CCCCTGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTTTCTTTCT
Found at i:4402096 original size:5 final size:5
Alignment explanation
Indices: 4402086--4402125 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
4402076 TCTTTAATTG
*
4402086 TAATA TAATA TAATA TAATA TAATA TAATA TAACA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
4402126 ATATTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:4402973 original size:23 final size:23
Alignment explanation
Indices: 4402929--4402973 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4402919 TTATATTAAA
**
4402929 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAAAATAAATATG
*
4402952 ATTAAAAATAAAAAATATATAT
1 ATTAAAAATAAAAAATAAATAT
4402974 TTAGTATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTAAAAATAAAAAATAAATATG
Found at i:4404301 original size:19 final size:19
Alignment explanation
Indices: 4404277--4404316 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4404267 GTGATTATCT
4404277 TAATATTAAATAAATTTAA
1 TAATATTAAATAAATTTAA
** *
4404296 TAATATTCTATTAATTTAA
1 TAATATTAAATAAATTTAA
4404315 TA
1 TA
4404317 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATTAAATAAATTTAA
Found at i:4405873 original size:31 final size:29
Alignment explanation
Indices: 4405835--4405908 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
4405825 TCTATAAAAA
* *
4405835 TAGTCACTTTTGTTTGCTCAAGGTTACATTT
1 TAGTCACTTATGTTTG--AAAGGTTACATTT
* *
4405866 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
4405895 TAGTCACTTATGTT
1 TAGTCACTTATGTT
4405909 ATTATTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:4406792 original size:17 final size:17
Alignment explanation
Indices: 4406772--4406805 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4406762 AGGTTTAGGT
4406772 TTAAAATTTTTAATTAA
1 TTAAAATTTTTAATTAA
**
4406789 TTAATTTTTTTAATTAA
1 TTAAAATTTTTAATTAA
4406806 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAAATTTTTAATTAA
Found at i:4411449 original size:29 final size:30
Alignment explanation
Indices: 4411409--4411474 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
4411399 ATGAATAGAT
* *
4411409 TTTTTTATTATTTTATGAGAG-TTAATTGA
1 TTTTTAATTATTTTAGGAGAGTTTAATTGA
4411438 TTTTTAATTATTTTAGGAGAGTTTAATTGA
1 TTTTTAATTATTTTAGGAGAGTTTAATTGA
4411468 TTTTTAA
1 TTTTTAA
4411475 GGATTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.58
Consensus pattern (30 bp):
TTTTTAATTATTTTAGGAGAGTTTAATTGA
Found at i:4411967 original size:27 final size:27
Alignment explanation
Indices: 4411937--4411990 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4411927 CATTGAATCA
4411937 AAGTTTATGTATAAATTTGATATCTAT
1 AAGTTTATGTATAAATTTGATATCTAT
4411964 AAGTTTATGTATAAATTTGATATCTAT
1 AAGTTTATGTATAAATTTGATATCTAT
4411991 TCCTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (27 bp):
AAGTTTATGTATAAATTTGATATCTAT
Found at i:4412201 original size:31 final size:31
Alignment explanation
Indices: 4412134--4412194 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
4412124 ATATGTTATG
* *
4412134 AAATAATGAAAATGCTAAATAAATATTATAA
1 AAATAATGAAAATGATAAATAAATATTAAAA
*
4412165 AAATAATTAAAATGATAAA-AAATA-TAAAA
1 AAATAATGAAAATGATAAATAAATATTAAAA
4412194 A
1 A
4412195 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 5 0.19
31 17 0.63
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (31 bp):
AAATAATGAAAATGATAAATAAATATTAAAA
Found at i:4412615 original size:17 final size:18
Alignment explanation
Indices: 4412580--4412615 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4412570 TATAAGTTGT
*
4412580 TAAAAAATTTTAATGTTA
1 TAAAAAATTTAAATGTTA
4412598 TAAAAAATTTAAAT-TTA
1 TAAAAAATTTAAATGTTA
4412615 T
1 T
4412616 TGTCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAAAAATTTAAATGTTA
Found at i:4414535 original size:28 final size:27
Alignment explanation
Indices: 4414486--4414541 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
4414476 TTCGTATAAC
* *
4414486 TAAATTTTGTATATTTATATGTATGAAT
1 TAAATATTGTATATTGATATGT-TGAAT
4414514 TAAATATTGTATATGTGA-ATGTTGAAT
1 TAAATATTGTATAT-TGATATGTTGAAT
4414541 T
1 T
4414542 GTGTAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 17 0.68
29 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (27 bp):
TAAATATTGTATATTGATATGTTGAAT
Found at i:4414889 original size:25 final size:24
Alignment explanation
Indices: 4414853--4414905 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
4414843 ACATACCGCA
4414853 GCTCTTTATGAGCATCCTGATATAG
1 GCTCTTTATGAGCATCCTGATAT-G
* * *
4414878 GCTCTTTGTGAGCTTCTTGATATG
1 GCTCTTTATGAGCATCCTGATATG
4414902 GCTC
1 GCTC
4414906 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.40
Consensus pattern (24 bp):
GCTCTTTATGAGCATCCTGATATG
Found at i:4417147 original size:16 final size:16
Alignment explanation
Indices: 4417101--4417153 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
4417091 TGATGTTAAA
4417101 ATTTATTATTATTT-TT
1 ATTTATT-TTATTTATT
*
4417117 ATATATTTGTATTTATT
1 ATTTATTT-TATTTATT
* *
4417134 ATTTATTTTTTTTATA
1 ATTTATTTTATTTATT
4417150 ATTT
1 ATTT
4417154 TTATATATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 21 0.68
17 9 0.29
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
ATTTATTTTATTTATT
Found at i:4417183 original size:39 final size:39
Alignment explanation
Indices: 4417106--4417183 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
4417096 TTAAAATTTA
* *
4417106 TTATTATTTTTATATATTTGTATTTATTATTTATTTTTT
1 TTATAATTTTTATATATTAGTATTTATTATTTATTTTTT
4417145 TTATAATTTTTATATA-TAGTATATT-TTATAATTATTTTT
1 TTATAATTTTTATATATTAGTAT-TTATTAT--TTATTTTT
4417184 GAATATGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 9 0.26
39 17 0.50
40 8 0.24
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (39 bp):
TTATAATTTTTATATATTAGTATTTATTATTTATTTTTT
Found at i:4425160 original size:20 final size:20
Alignment explanation
Indices: 4425135--4425195 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
4425125 AACAACATAC
4425135 TATATGTTGGAGGACACACT
1 TATATGTTGGAGGACACACT
4425155 TATATGTTGGAGGACACACT
1 TATATGTTGGAGGACACACT
4425175 TATATGTTGGAGGACACACT
1 TATATGTTGGAGGACACACT
4425195 T
1 T
4425196 TTGATCATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (20 bp):
TATATGTTGGAGGACACACT
Found at i:4445784 original size:20 final size:19
Alignment explanation
Indices: 4445710--4445827 Score: 79
Period size: 18 Copynumber: 6.3 Consensus size: 19
4445700 ATACTCACTC
*
4445710 TCTTTTTCAATTTTC-TTT
1 TCTTTTTCAATTCTCTTTT
**
4445728 TCTTAATCAATT-TCTTTT
1 TCTTTTTCAATTCTCTTTT
4445746 TCTTTTTCAATTC-CGTTTT
1 TCTTTTTCAATTCTC-TTTT
*
4445765 TCTTTTTCTCATTCTCTTTT
1 TCTTTTTC-AATTCTCTTTT
4445785 TGCTCTATTTCACA--CTCTTTT
1 T-CT-T-TTTCA-ATTCTCTTTT
* *
4445806 TC--TTTCATTTCTTTTTT
1 TCTTTTTCAATTCTCTTTT
4445823 TCTTT
1 TCTTT
4445828 CAAATTCTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
16 5 0.06
17 10 0.13
18 24 0.30
19 13 0.16
20 10 0.13
21 11 0.14
22 1 0.01
23 5 0.06
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (19 bp):
TCTTTTTCAATTCTCTTTT
Found at i:4445835 original size:18 final size:17
Alignment explanation
Indices: 4445802--4445837 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4445792 TTTCACACTC
*
4445802 TTTTTCTTTCATTTCTT
1 TTTTTCTTTCAATTCTT
4445819 TTTTTCTTTCAAATTCTT
1 TTTTTCTTTC-AATTCTT
4445837 T
1 T
4445838 CTTACATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTCTTTCAATTCTT
Found at i:4452202 original size:5 final size:6
Alignment explanation
Indices: 4452186--4452210 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4452176 GAGAATTATA
4452186 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
4452211 AAAATTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:4452287 original size:13 final size:13
Alignment explanation
Indices: 4452269--4452296 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4452259 TTAATTTGCC
4452269 ATTTTGAAATAAA
1 ATTTTGAAATAAA
4452282 ATTTTGAAATAAA
1 ATTTTGAAATAAA
4452295 AT
1 AT
4452297 AAAAACTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTTGAAATAAA
Found at i:4453950 original size:13 final size:13
Alignment explanation
Indices: 4453932--4453995 Score: 119
Period size: 13 Copynumber: 4.9 Consensus size: 13
4453922 ACACTCAAAA
4453932 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
4453945 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
4453958 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
4453971 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
4453984 TTCTCAAAAGCA
1 TTCTCAAAAGCA
4453996 ATGAAGAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.23
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:4459767 original size:24 final size:24
Alignment explanation
Indices: 4459740--4459791 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4459730 TTAGTAAGTC
*
4459740 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4459764 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4459788 AAAT
1 AAAT
4459792 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4461736 original size:24 final size:24
Alignment explanation
Indices: 4461709--4461760 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4461699 TTAGTAAGTC
*
4461709 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4461733 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4461757 AAAT
1 AAAT
4461761 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4463305 original size:5 final size:5
Alignment explanation
Indices: 4463295--4463326 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4463285 TTGTGTGTTC
4463295 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4463327 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4463309 original size:9 final size:9
Alignment explanation
Indices: 4463295--4463325 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4463285 TTGTGTGTTC
4463295 TTTATTTTA
1 TTTATTTTA
4463304 TTTATTTTA
1 TTTATTTTA
4463313 TTTTATTTTA
1 -TTTATTTTA
4463323 TTT
1 TTT
4463326 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4467757 original size:5 final size:5
Alignment explanation
Indices: 4467747--4467778 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4467737 TTGTGTGTTC
4467747 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4467779 TCACAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4467761 original size:9 final size:9
Alignment explanation
Indices: 4467747--4467777 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4467737 TTGTGTGTTC
4467747 TTTATTTTA
1 TTTATTTTA
4467756 TTTATTTTA
1 TTTATTTTA
4467765 TTTTATTTTA
1 -TTTATTTTA
4467775 TTT
1 TTT
4467778 TTCACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4468755 original size:40 final size:38
Alignment explanation
Indices: 4468695--4468835 Score: 108
Period size: 40 Copynumber: 3.6 Consensus size: 38
4468685 AACACACTAG
* * *
4468695 TTTGGCACCTAGTGCCTCATCAGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATC-GATAA-TCGAAGTAATAA
* * *
4468735 TTTGACACCTAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATC-GAT-AATCGAAGTAATAA
* *
4468773 -TTGATACCCAGTGTCTCATCGAATTAATCTGAAGTAGTAA
1 TTTGACACCCAGTGTCTCATCG-A-TAATC-GAAGTAATAA
* *
4468813 ATTGACACCCAGTTTCTCATCGA
1 TTTGACACCCAGTGTCTCATCGA
4468836 CTCGAAGTTG
Statistics
Matches: 82, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
36 1 0.01
37 21 0.26
38 8 0.10
39 1 0.01
40 30 0.37
41 21 0.26
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (38 bp):
TTTGACACCCAGTGTCTCATCGATAATCGAAGTAATAA
Found at i:4469022 original size:24 final size:24
Alignment explanation
Indices: 4468993--4469039 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4468983 TATATATACC
4468993 AATTCAATCA-ATA-TAAATTCAATA
1 AATTC-ATCACATACTAAA-TCAATA
4469017 AATTCATCACATACTAAATCAAT
1 AATTCATCACATACTAAATCAAT
4469040 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCATCACATACTAAATCAATA
Found at i:4469787 original size:36 final size:36
Alignment explanation
Indices: 4469710--4469787 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
4469700 TTCCCCCCCT
* *
4469710 TTTTTTATATTATAATATATATACTTAAACATTAAG
1 TTTTTTATATTATAATATATATACATAAACATTAAA
*
4469746 GTTTTTATATTATAATATATATA-ATAAAC-TTACACA
1 TTTTTTATATTATAATATATATACATAAACATTA-A-A
4469782 TTTTTT
1 TTTTTT
4469788 TAATCTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 3 0.08
35 6 0.17
36 27 0.75
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTTTTATATTATAATATATATACATAAACATTAAA
Found at i:4479363 original size:21 final size:21
Alignment explanation
Indices: 4479340--4479381 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4479330 TATTTTTATT
*
4479340 AAATTAATTTATATAATAAATA
1 AAATAAATTT-TATAATAAATA
*
4479362 AAATAAATTTTATATTAAAT
1 AAATAAATTTTATAATAAAT
4479382 TACTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATAAATTTTATAATAAATA
Found at i:4483283 original size:2 final size:2
Alignment explanation
Indices: 4483276--4483303 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4483266 AGTTAATAAC
4483276 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4483304 TATATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4487006 original size:31 final size:29
Alignment explanation
Indices: 4486951--4487008 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
4486941 GGCCCAACCC
*
4486951 ATAAGGGTTAAACTTTTCAAAATACTTAT
1 ATAAGGGTTAAACTTTACAAAATACTTAT
*
4486980 ATAAGGGCTTAACCTTTACAAAAATACTT
1 ATAAGGG-TTAAACTTTAC-AAAATACTT
4487009 TAATGAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 9 0.36
31 9 0.36
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (29 bp):
ATAAGGGTTAAACTTTACAAAATACTTAT
Found at i:4500528 original size:44 final size:44
Alignment explanation
Indices: 4500479--4500565 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
4500469 CACCTATTCA
4500479 ATATTCACTTGTTCTCAACCCTTTTGCGTAACCGTACCTTACTC
1 ATATTCACTTGTTCTCAACCCTTTTGCGTAACCGTACCTTACTC
4500523 ATATTCACTTGTTCTCAACCCTTTTGCGTAACCGTACCTTACT
1 ATATTCACTTGTTCTCAACCCTTTTGCGTAACCGTACCTTACT
4500566 TACATAACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.21, C:0.31, G:0.09, T:0.39
Consensus pattern (44 bp):
ATATTCACTTGTTCTCAACCCTTTTGCGTAACCGTACCTTACTC
Found at i:4500683 original size:16 final size:15
Alignment explanation
Indices: 4500662--4500701 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
4500652 TACTGCCAAT
4500662 TGCTACATTGAATTAC
1 TGCTACATTG-ATTAC
*
4500678 TGCTACATTGATTGC
1 TGCTACATTGATTAC
*
4500693 TACTACATT
1 TGCTACATT
4500702 TGTTGGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (15 bp):
TGCTACATTGATTAC
Found at i:4503980 original size:28 final size:28
Alignment explanation
Indices: 4503940--4503996 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
4503930 CATCCAATCA
*
4503940 TTATTTTTATATTGCTATTGAAATGTTT
1 TTATTTTTATATTGCTAGTGAAATGTTT
*
4503968 TTATTTTTATATTGGTAGTGAAATGTTT
1 TTATTTTTATATTGCTAGTGAAATGTTT
4503996 T
1 T
4503997 AAGGATTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.60
Consensus pattern (28 bp):
TTATTTTTATATTGCTAGTGAAATGTTT
Found at i:4514338 original size:69 final size:68
Alignment explanation
Indices: 4514223--4514622 Score: 363
Period size: 69 Copynumber: 5.8 Consensus size: 68
4514213 AAATTATCGT
* ** * * * *
4514223 CTGTAAAATTAAGGTTCACAATTGAAGGGCTGCGACCTCTACCACAGTTAGCAAGAGCAATGTTT
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATG-CT
4514288 CCAG
65 CCAG
* *
4514292 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCAGCACAGTTAGCGAGAGCAATGGTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
4514357 TCAG
66 -CAG
* * * * * * *
4514361 CTGTAAAATTAAGGTTCGCAGGCAAAGAGCTGTGACCTCCATCATAGTTAGTGAGAGCAATACTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
*
4514426 CTAA
66 C-AG
** * * * * *
4514430 CTGTAAAATTAAGGTTCATAGGCGAAGAGCCGCAACCTTCACCACAGTTAGCGAGAGCAAAGCTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
4514495 CTAG
66 C-AG
** * * * ** * * * *
4514499 CTAAAAAATTAAGGTTTGCAGGCTAAGAGCCACGACCTCTAGCACAATTAGCGAGAGCAAAGCTC
1 CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
*
4514564 TCAA
66 -CAG
* * * *
4514568 CTATAAAATTAAGGTTCG-TAGACGAAGAG-TCGCGACCTCCAACATAGTTAGCGAG
1 CTGTAAAATTAAGGTTCGCAAG-CGAAGAGCT-GCGACCTCCACCACAGTTAGCGAG
4514623 GGTAAACCTC
Statistics
Matches: 272, Mismatches: 54, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
68 4 0.01
69 267 0.98
70 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (68 bp):
CTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCACCACAGTTAGCGAGAGCAATGCTC
CAG
Found at i:4514578 original size:207 final size:207
Alignment explanation
Indices: 4514223--4514618 Score: 492
Period size: 207 Copynumber: 1.9 Consensus size: 207
4514213 AAATTATCGT
** * * * * *
4514223 CTGTAAAATTAAGGTTCACAATTGAAGGGCTGCGACCTCTACCACAGTTAGCAAGAGCAATGTTT
1 CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCTACCACAGTTAGCAAGAGCAAAGTCT
** ** * *
4514288 CCAGCTGTAAAATTAAGGTTCGCAAGCGAAGAGCTGCGACCTCCAGCACAGTTAGCGAGAGCAAT
66 CCAGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCAAA
* * * * * *
4514353 GGTCTCAGCTGTAAAATTAAGGTTCGCAGGCAAAGAG-CTGTGACCTCCATCATAGTTAGTGAGA
131 GCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTC-GCGACCTCCAACATAGTTAGTGAGA
4514417 GCAATACTCCTAA
195 GCAATACTCCTAA
* * *
4514430 CTGTAAAATTAAGGTTCATAGGCGAAGAGCCGCAACCT-TCACCACAGTTAGCGAGAGCAAAG-C
1 CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCT-ACCACAGTTAGCAAGAGCAAAGTC
* * * *
4514493 TCCTAGCTAAAAAATTAAGGTTTGCAGGCTAAGAGCCACGACCTCTAGCACAATTAGCGAGAGCA
65 TCC-AGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCA
* *
4514558 AAGCTCTCAACTATAAAATTAAGGTTCGTAGACGAAGAGTCGCGACCTCCAACATAGTTAG
129 AAGCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTCGCGACCTCCAACATAGTTAG
4514619 CGAGGGTAAA
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
206 4 0.03
207 153 0.97
208 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (207 bp):
CTGTAAAATTAAGGTTCACAAGCGAAGAGCCGCAACCTCTACCACAGTTAGCAAGAGCAAAGTCT
CCAGCTAAAAAATTAAGGTTCGCAAGCGAAGAGCCACGACCTCCAGCACAATTAGCGAGAGCAAA
GCTCTCAACTATAAAATTAAGGTTCGCAGACAAAGAGTCGCGACCTCCAACATAGTTAGTGAGAG
CAATACTCCTAA
Found at i:4520542 original size:6 final size:7
Alignment explanation
Indices: 4520525--4520551 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4520515 TGGATGTTAA
4520525 AAAAAAT
1 AAAAAAT
4520532 AAAAAAT
1 AAAAAAT
4520539 AAAAAAT
1 AAAAAAT
4520546 AAAAAA
1 AAAAAA
4520552 ATACAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:4520663 original size:13 final size:14
Alignment explanation
Indices: 4520628--4520666 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
4520618 GAAGATATTT
4520628 ATATATTATATATAA
1 ATATATTAT-TATAA
*
4520643 ATAAATTATTAT-A
1 ATATATTATTATAA
4520656 ATATATTATTA
1 ATATATTATTA
4520667 GTAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTATTATAA
Found at i:4520714 original size:21 final size:21
Alignment explanation
Indices: 4520688--4520728 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4520678 AAATAAAAGA
*
4520688 AAAAGAATAAAGAAAAGAAAC
1 AAAAGAACAAAGAAAAGAAAC
4520709 AAAAGAACAAAGAAAAGAAA
1 AAAAGAACAAAGAAAAGAAA
4520729 ACAGAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAGAACAAAGAAAAGAAAC
Found at i:4530763 original size:11 final size:11
Alignment explanation
Indices: 4530747--4530799 Score: 63
Period size: 11 Copynumber: 4.6 Consensus size: 11
4530737 CTTCAAAAAT
4530747 AAATAAAAGTA
1 AAATAAAAGTA
4530758 AAATAAAAGTA
1 AAATAAAAGTA
*
4530769 AAATTAAAAAGAA
1 AAA-T-AAAAGTA
4530782 AAATAATAA-TA
1 AAATAA-AAGTA
4530793 AAATAAA
1 AAATAAA
4530800 TGGACTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 4 0.11
13 9 0.24
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAATAAAAGTA
Found at i:4530784 original size:24 final size:24
Alignment explanation
Indices: 4530751--4530796 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4530741 AAAAATAAAT
*
4530751 AAAAGTAAAATAA-AAGTAAAATTA
1 AAAAGAAAAATAATAA-TAAAATTA
4530775 AAAAGAAAAATAATAATAAAAT
1 AAAAGAAAAATAATAATAAAAT
4530797 AAATGGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (24 bp):
AAAAGAAAAATAATAATAAAATTA
Found at i:4530795 original size:12 final size:11
Alignment explanation
Indices: 4530741--4530799 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
4530731 ATAAGTCTTC
4530741 AAAAAT-AAAT
1 AAAAATAAAAT
*
4530751 AAAAGTAAAAT
1 AAAAATAAAAT
*
4530762 AAAAGTAAAATT
1 AAAAATAAAA-T
*
4530774 AAAAAGAAAAAT
1 AAAAA-TAAAAT
*
4530786 AATAATAAAAT
1 AAAAATAAAAT
4530797 AAA
1 AAA
4530800 TGGACTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 5 0.12
11 21 0.52
12 10 0.25
13 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:4538437 original size:24 final size:23
Alignment explanation
Indices: 4538402--4538450 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
4538392 ACAAGGTCTT
*
4538402 ATTTTCTTGCTT-GAGTTCTAGAA
1 ATTTTCTTGCTTCGAG-TCTAAAA
*
4538425 ATTTTTTTCGCTTCGAGTCTAAAA
1 ATTTTCTT-GCTTCGAGTCTAAAA
4538449 AT
1 AT
4538451 CTTTGACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 12 0.55
25 3 0.14
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (23 bp):
ATTTTCTTGCTTCGAGTCTAAAA
Found at i:4549756 original size:13 final size:14
Alignment explanation
Indices: 4549733--4549762 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4549723 GACTTGTTCG
4549733 TATTAATTTTTTTA
1 TATTAATTTTTTTA
4549747 TATT-ATTTTTTTA
1 TATTAATTTTTTTA
4549760 TAT
1 TAT
4549763 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTAATTTTTTTA
Found at i:4555516 original size:12 final size:12
Alignment explanation
Indices: 4555499--4555523 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4555489 TTACAGCTAG
4555499 TCTAGGAGTATT
1 TCTAGGAGTATT
4555511 TCTAGGAGTATT
1 TCTAGGAGTATT
4555523 T
1 T
4555524 TGGTGATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TCTAGGAGTATT
Found at i:4559140 original size:126 final size:126
Alignment explanation
Indices: 4558868--4559304 Score: 562
Period size: 122 Copynumber: 3.5 Consensus size: 126
4558858 TTAAGTTCAT
* * * *
4558868 TGCATCCTGCTTGAAGCATTTTTAACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
1 TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
* * *
4558933 AGGAACTA-TGTAGAAAAAGAGCGTCCACGTGGGAGTTTTTTTCTACAATTTTGTTGACAA
66 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
* *
4558993 TGCA-TCTTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTT
1 TGCATTC-TACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTT
* * * **
4559057 CATGAACTACTATAGAAAAAGAGTGTCCACGTGATAGCTTTTTTCTATAATTTTGTTGACAG
65 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
* * **
4559119 TGTATTCTACTTGAAGCGTTTTTGACACTA----TTCATAAATGTCTTCTCAAAATTATTTTTTC
1 TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
* * * * * * *
4559180 AGGAACTACTGTAGAAAAAGAACATCCACGTGGGAGCTTTTTTTTGTATTTTTGCTGATAG
66 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
* * **
4559241 TGCATCCTACTTGAAGCGTTTTTGATACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
1 TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTT
4559305 GGGGGTAAAA
Statistics
Matches: 271, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
122 104 0.38
124 1 0.00
125 66 0.24
126 98 0.36
127 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (126 bp):
TGCATTCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTC
AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCTATAATTTTGTTGACAG
Found at i:4559438 original size:30 final size:28
Alignment explanation
Indices: 4559393--4559596 Score: 114
Period size: 34 Copynumber: 6.7 Consensus size: 28
4559383 ATTTAACCAT
4559393 AAACCCTAAACCCTAATTTAATTTATTTA
1 AAACCCTAAA-CCTAATTTAATTTATTTA
4559422 AAACCCTAGAATCCTAAATTACTTAATTTATTTAA
1 AAACCCTA-AA-CCT-AA-T--TTAATTTATTT-A
*
4559457 AAACCATAAACTCTAATTTAATTTATTTA
1 AAACCCTAAAC-CTAATTTAATTTATTTA
*
4559486 AAA-CCT-----TATTTTAATTTATTTA
1 AAACCCTAAACCTAATTTAATTTATTTA
* *
4559508 AAACCTATAAACCTTAAACCTTAATTTATTTA
1 AAACC-CTAAACC-T-AA-TTTAATTTATTTA
*
4559540 AAACCTTAAAAACCCTAATTTATTTAATTTATTTAA
1 AAACCCT--AAA-CCT-A---ATTTAATTTATTT-A
*
4559576 AAACCATAAACCCTAATTTAA
1 AAACCCTAAA-CCTAATTTAA
4559597 ATAATTTTTA
Statistics
Matches: 141, Mismatches: 10, Indels: 47
0.71 0.05 0.24
Matches are distributed among these distances:
22 18 0.13
23 1 0.01
24 1 0.01
28 2 0.01
29 12 0.09
30 23 0.16
31 4 0.03
32 19 0.13
33 10 0.07
34 24 0.17
35 19 0.13
36 8 0.06
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (28 bp):
AAACCCTAAACCTAATTTAATTTATTTA
Found at i:4559501 original size:52 final size:54
Alignment explanation
Indices: 4559444--4559547 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
4559434 CCTAAATTAC
*
4559444 TTAATTTATTTAAAAACC-ATAAA-CTCT-AA-TTTAATTTATTTAAAACCTTATT
1 TTAATTTATTT-AAAACCTATAAACCT-TAAACCTTAATTTATTTAAAACCTTATT
4559496 TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACCTTA
1 TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACCTTA
4559548 AAAACCCTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
51 6 0.13
52 17 0.36
53 4 0.09
54 20 0.43
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (54 bp):
TTAATTTATTTAAAACCTATAAACCTTAAACCTTAATTTATTTAAAACCTTATT
Found at i:4559602 original size:34 final size:35
Alignment explanation
Indices: 4559529--4559611 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
4559519 CCTTAAACCT
**
4559529 TAATTTATTT-AAAACCTTAAAAACCCTAATTTATT
1 TAATTTATTTAAAAACC-TAAAAACCCTAATTTAAA
*
4559564 TAATTTATTTAAAAACC-ATAAACCCTAATTTAAA
1 TAATTTATTTAAAAACCTAAAAACCCTAATTTAAA
4559598 TAATTT-TTATAAAA
1 TAATTTATT-TAAAA
4559612 TAACACCAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.05
34 25 0.58
35 10 0.23
36 6 0.14
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (35 bp):
TAATTTATTTAAAAACCTAAAAACCCTAATTTAAA
Found at i:4561088 original size:57 final size:57
Alignment explanation
Indices: 4561000--4561120 Score: 242
Period size: 57 Copynumber: 2.1 Consensus size: 57
4560990 CAACCAAGAA
4561000 AAAATCAGAAATAAGGTTGGCCATTCTCCATCGATTGTGGAACTATAAGACTTAAGC
1 AAAATCAGAAATAAGGTTGGCCATTCTCCATCGATTGTGGAACTATAAGACTTAAGC
4561057 AAAATCAGAAATAAGGTTGGCCATTCTCCATCGATTGTGGAACTATAAGACTTAAGC
1 AAAATCAGAAATAAGGTTGGCCATTCTCCATCGATTGTGGAACTATAAGACTTAAGC
4561114 AAAATCA
1 AAAATCA
4561121 TTTTAACTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (57 bp):
AAAATCAGAAATAAGGTTGGCCATTCTCCATCGATTGTGGAACTATAAGACTTAAGC
Found at i:4570703 original size:18 final size:20
Alignment explanation
Indices: 4570661--4570697 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4570651 ATATTTTATG
*
4570661 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
4570680 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
4570698 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:4572901 original size:46 final size:46
Alignment explanation
Indices: 4572849--4573169 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
4572839 AGTGTGCTCT
4572849 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4572895 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
4572941 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
4572987 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *** *
4573033 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
4573079 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * * * *
4573125 ATGACAAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
4573170 TCATGTCAAA
Statistics
Matches: 249, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 216 0.87
47 33 0.13
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:4575733 original size:24 final size:25
Alignment explanation
Indices: 4575706--4575753 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
4575696 CCTGAATTAC
4575706 AAATAGAAAATAAAAC-TAAGTAAG
1 AAATAGAAAATAAAACTTAAGTAAG
*
4575730 AAATGGAAAATAAAACTTAAGTAA
1 AAATAGAAAATAAAACTTAAGTAA
4575754 AAACTATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (25 bp):
AAATAGAAAATAAAACTTAAGTAAG
Found at i:4578226 original size:53 final size:53
Alignment explanation
Indices: 4578085--4578299 Score: 216
Period size: 53 Copynumber: 4.2 Consensus size: 53
4578075 TGTGCGCCCT
* ** *
4578085 TATAAGACCATAGTTGGGCTATGGCATCTGTGCAATGTGAT-ACGTG-TTCCCG
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATT-CCG
* * * *
4578137 TATAAGACCATAGTTGGGCTATGGCTTCGGTATGATGTGATAATGTGATTCCA
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
* * *
4578190 TATAAGACCATAGCTGGGCTATAGCGTCAGTGTGATGTGATAATGTGATTCCG
1 TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
* *
4578243 TATAAAACCATA-TATGGGATATGGCATC-G-GT-AT-T-AT-ATGTGA-TCCG
1 TATAAGACCATAGT-TGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
*
4578289 TGTAAGACCAT
1 TATAAGACCAT
4578300 GGGATGGATA
Statistics
Matches: 140, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
46 13 0.09
47 6 0.04
48 2 0.01
49 1 0.01
50 2 0.01
51 2 0.01
52 37 0.26
53 75 0.54
54 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (53 bp):
TATAAGACCATAGTTGGGCTATGGCATCAGTGTGATGTGATAATGTGATTCCG
Found at i:4579192 original size:37 final size:37
Alignment explanation
Indices: 4579140--4579213 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
4579130 TGGCTTAGCC
*
4579140 ACATGGGCGTATGCCTAGGCCATGTGCCGCTCTGATA
1 ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
* * *
4579177 ACATGGGTGTGTGCCTAGGCCGTGTGCCCCTCTGATA
1 ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
4579214 CTTAAGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.16, C:0.27, G:0.31, T:0.26
Consensus pattern (37 bp):
ACATGGGCGTATGCCTAGGCCATGTGCCCCTCTGATA
Found at i:4579815 original size:22 final size:22
Alignment explanation
Indices: 4579787--4579841 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
4579777 TTCTTCTTTG
4579787 TTTTCTCCTTTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
4579809 TTTTCTCCTCTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
4579831 TATT-TCCTTTT
1 TTTTCTCCTTTT
4579842 TCCTTATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTCTCCTTTTCTCCAAAATT
Found at i:4590422 original size:16 final size:14
Alignment explanation
Indices: 4590399--4590438 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
4590389 CGTCTTTCCC
4590399 TCTTTCTTTTCTCAT
1 TCTTTCTTTTCTC-T
4590414 TCTTTTCTTTTTCTCT
1 TC-TTTC-TTTTCTCT
4590430 TCTTTCTTT
1 TCTTTCTTT
4590439 AACCAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 6 0.26
16 7 0.30
17 7 0.30
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTCTTTTCTCT
Found at i:4591436 original size:21 final size:21
Alignment explanation
Indices: 4591407--4591449 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4591397 ATAAACAATA
*
4591407 TAATTGTTTTG-CTTTTTAACT
1 TAATGGTTTTGAC-TTTTAACT
4591428 TAATGGTTTTGACTTTTAACT
1 TAATGGTTTTGACTTTTAACT
4591449 T
1 T
4591450 TAGAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (21 bp):
TAATGGTTTTGACTTTTAACT
Found at i:4592724 original size:10 final size:10
Alignment explanation
Indices: 4592692--4592733 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 10
4592682 GTCTGATTAA
4592692 TTTTAATTTT
1 TTTTAATTTT
4592702 AATTTTAAATTTT
1 --TTTT-AATTTT
4592715 TTTT-ATTTT
1 TTTTAATTTT
4592724 TTTTAATTTT
1 TTTTAATTTT
4592734 CCAAAACTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.32
10 5 0.18
11 4 0.14
12 4 0.14
13 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:4594274 original size:42 final size:42
Alignment explanation
Indices: 4594211--4594337 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
4594201 CTTCGTTTTC
** * *
4594211 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
4594254 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
4594295 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
4594336 TC
1 TC
4594338 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:4594399 original size:47 final size:46
Alignment explanation
Indices: 4594296--4594417 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 46
4594286 ATTCATATAT
* * * * *
4594296 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
4594342 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
4594389 CGATGCCATATCCCAGATATGGTCTTATA
1 CGATGCCATATCCCAGATATGGTCTTATA
4594418 TGGAAATCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 26 0.39
47 40 0.61
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:4594486 original size:31 final size:31
Alignment explanation
Indices: 4594451--4594591 Score: 219
Period size: 31 Copynumber: 4.5 Consensus size: 31
4594441 CTTGTAGCGA
* *
4594451 AGCTACCACTATTCACTGATAAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
*
4594482 AGCTACCATTTTTCACTGATCAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
4594513 AGCTACCACTTTTCACTGATCAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
* ** *
4594544 AACTACCACTTTTCACTGATCAGGTAGTTGA
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
4594575 AGCTACCACTTTTCACT
1 AGCTACCACTTTTCACT
4594592 TGTCATTTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGCCGG
Found at i:4594671 original size:50 final size:51
Alignment explanation
Indices: 4594573--4594695 Score: 196
Period size: 50 Copynumber: 2.4 Consensus size: 51
4594563 TCAGGTAGTT
* *
4594573 GAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
*
4594624 GAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGTGTAGCC
4594674 GAAGCTATCACTTATCACTTGT
1 GAAGCTATCACTTATCACTTGT
4594696 TGCCATGGTC
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
50 45 0.67
51 22 0.33
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (51 bp):
GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
Found at i:4594830 original size:14 final size:15
Alignment explanation
Indices: 4594811--4594839 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4594801 TTTTATCATC
4594811 AACACAT-ATGAAAT
1 AACACATCATGAAAT
4594825 AACACATCATGAAAT
1 AACACATCATGAAAT
4594840 TCATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (15 bp):
AACACATCATGAAAT
Found at i:4605213 original size:41 final size:41
Alignment explanation
Indices: 4605089--4605395 Score: 386
Period size: 41 Copynumber: 7.5 Consensus size: 41
4605079 ATAACGGCAT
* * * * *
4605089 TTTTAGTAAGACGCCGCTAAA-AACAGAGCAATAGCGGTG-
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* * * * *
4605128 TTTTAGTAAAAAGCACCGCTAAA-AACAAAGCATTAGTGGCGC
1 TTTTGGT-AAAA-CGCCGCTAAAGACCAGAGCATTAGCGGCGC
* *
4605170 TTTTGGTAAAACGCCGCTAAAGACCAGAGTATTATCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
** *
4605211 TTTTATTAAAACGCCGTTAAAGACCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
*
4605252 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGACGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
4605293 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
** * *
4605334 TTTTATTAAAACGACGCTAAAGACCAGAACATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
*
4605375 TTTTGGTAAAACACCGCTAAA
1 TTTTGGTAAAACGCCGCTAAA
4605396 AGTCATATAA
Statistics
Matches: 233, Mismatches: 31, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
39 7 0.03
40 12 0.05
41 208 0.89
42 6 0.03
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (41 bp):
TTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
Found at i:4605294 original size:123 final size:122
Alignment explanation
Indices: 4605089--4605396 Score: 431
Period size: 123 Copynumber: 2.5 Consensus size: 122
4605079 ATAACGGCAT
* * * * * *
4605089 TTTTAGTAAGACGCCGCTAAA-AACAGAGCAATAGCGGTG-TTTTAGTAAAAAGCACCGCTAAAA
1 TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT-AAAA-CACCGCTAAAA
* * * *
4605152 ACAAAGCATTAGTGGCGCTTTTGGTAAAACGCCGCTAAAGACCAGAGTATTATCGGCGC
64 ACAAAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* * *
4605211 TTTTATTAAAACGCCGTTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGAC
1 TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACACCGCTAAA-AA
*
4605276 CAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
65 CAAAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
* *
4605334 TTTTATTAAAACGACGCTAAAGACCAGAACATTAGCGGCGCTTTTGGTAAAACACCGCTAAAA
1 TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACACCGCTAAAA
4605397 GTCATATAAC
Statistics
Matches: 165, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
122 28 0.17
123 131 0.79
124 6 0.04
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (122 bp):
TTTTATTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTAAAACACCGCTAAAAAC
AAAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGC
Found at i:4605635 original size:21 final size:21
Alignment explanation
Indices: 4605558--4605635 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
4605548 TTATCATTGT
4605558 AGTTTAAG-GTTTATGGTTTAA
1 AGTTTAAGAGTTTATGGTTT-A
*
4605579 AGTTTATGAGTTAACTATGGTTTA
1 AGTTTAAGAGTT---TATGGTTTA
* * *
4605603 AG-ATATATAGTTTAGGGTTTA
1 AGTTTA-AGAGTTTATGGTTTA
4605624 AGTTTAAGAGTT
1 AGTTTAAGAGTT
4605636 AACTAGTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 22 0.50
22 5 0.11
23 2 0.05
24 7 0.16
25 8 0.18
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (21 bp):
AGTTTAAGAGTTTATGGTTTA
Found at i:4605944 original size:21 final size:21
Alignment explanation
Indices: 4605920--4605965 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4605910 TGATTTAATT
* *
4605920 TTTAAGGTTTGGAGATTAGGG
1 TTTAAGGTTTAGAGATTAGGC
* *
4605941 TTTAGGGTTTAGAGTTTAGGC
1 TTTAAGGTTTAGAGATTAGGC
4605962 TTTA
1 TTTA
4605966 TAATTTAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (21 bp):
TTTAAGGTTTAGAGATTAGGC
Found at i:4611506 original size:9 final size:9
Alignment explanation
Indices: 4611489--4611544 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
4611479 CTTCTCTCAT
4611489 ATAACTTAC
1 ATAACTTAC
*
4611498 ATAATTTAC
1 ATAACTTAC
*
4611507 ATAACTCAC
1 ATAACTTAC
*
4611516 ATAACGTAC
1 ATAACTTAC
4611525 ATAACAACTTAC
1 AT---AACTTAC
4611537 ATAACTTA
1 ATAACTTA
4611545 ACTAATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.79
12 8 0.21
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAACTTAC
Found at i:4617116 original size:21 final size:21
Alignment explanation
Indices: 4617090--4617137 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
4617080 TCAACTCAGA
4617090 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
4617111 GCGGAGGCAGCAGTGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
4617132 GAGGAG
1 GCGGAG
4617138 CAGAACAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.58, T:0.02
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:4617562 original size:43 final size:43
Alignment explanation
Indices: 4617430--4617612 Score: 158
Period size: 43 Copynumber: 4.3 Consensus size: 43
4617420 ACTGGGCAAA
* * * *
4617430 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTA-AAGACCAAGACTT
1 TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTC-T
* * * * ** * *
4617473 TTAGTGGCGCTGTTTTAAAAA-ACGCCACTA-AAGAACAAGACTT
1 TTAGCGGCG-TTTTTTAAAAATGCGCCGCTATAAGTCCTAGTC-T
* * * *
4617516 TTAGCGACGTTTTTTATATAA-GCGTCGCTATAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTA-AAAATGCGCCGCTATAAGTCCTAGTCT
4617559 TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTCT
1 TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTCT
4617602 TTAGCGGCGTT
1 TTAGCGGCGTT
4617613 ACATATAGCG
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
42 9 0.08
43 90 0.78
44 16 0.14
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTAAAAATGCGCCGCTATAAGTCCTAGTCT
Found at i:4627907 original size:18 final size:19
Alignment explanation
Indices: 4627881--4627916 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4627871 GAAGATATTA
*
4627881 TTTTGTTTTATT-ATTTAT
1 TTTTATTTTATTAATTTAT
4627899 TTTTATTTTATTAATTTA
1 TTTTATTTTATTAATTTA
4627917 GGATTAAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTATTTTATTAATTTAT
Found at i:4632986 original size:21 final size:21
Alignment explanation
Indices: 4632961--4633029 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4632951 TATAATGATT
4632961 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
4632982 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
4633002 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
4633022 ATTATTAT
1 ATTATTAT
4633030 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:4633042 original size:15 final size:14
Alignment explanation
Indices: 4633016--4633046 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4633006 TATGGTTTTA
4633016 TATTAGATTATTAT
1 TATTAGATTATTAT
4633030 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
4633045 TA
1 TA
4633047 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:4643834 original size:21 final size:19
Alignment explanation
Indices: 4643800--4643864 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 19
4643790 GCTTTCACAT
*
4643800 TAAAAAAATAATAAATAAA
1 TAAATAAATAATAAATAAA
*
4643819 TAAAT-AATAA-CAATAAA
1 TAAATAAATAATAAATAAA
4643836 -ATAATAAAT-ATAAATATAA
1 TA-AATAAATAATAAATA-AA
4643855 T-AATAAATAA
1 TAAATAAATAA
4643865 AATTTAAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
16 1 0.03
17 10 0.27
18 19 0.51
19 7 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAATAAATAATAAATAAA
Found at i:4643837 original size:18 final size:16
Alignment explanation
Indices: 4643800--4643867 Score: 72
Period size: 15 Copynumber: 4.4 Consensus size: 16
4643790 GCTTTCACAT
4643800 TAAAA-AAATAATAAA
1 TAAAATAAATAATAAA
4643815 T-AAATAAATAAT-AA
1 TAAAATAAATAATAAA
* *
4643829 CAATA-AAATAATAAA
1 TAAAATAAATAATAAA
4643844 TATAAATATAATAATAAA
1 TA-AAATA-AATAATAAA
4643862 TAAAAT
1 TAAAAT
4643868 TTAAGACGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 12 0.28
15 13 0.30
16 2 0.05
17 5 0.12
18 11 0.26
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATAAATAATAAA
Found at i:4643845 original size:29 final size:30
Alignment explanation
Indices: 4643800--4643867 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
4643790 GCTTTCACAT
4643800 TAAA-AAAATAAT-AA-ATAAATA-AATAA
1 TAAATAAAATAATAAATATAAATATAATAA
4643826 TAACAATAAAATAATAAATATAAATATAATAA
1 T-A-AATAAAATAATAAATATAAATATAATAA
4643858 TAAATAAAAT
1 TAAATAAAAT
4643868 TTAAGACGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 2 0.06
29 8 0.22
30 10 0.28
31 8 0.22
32 6 0.17
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (30 bp):
TAAATAAAATAATAAATATAAATATAATAA
Found at i:4644487 original size:13 final size:13
Alignment explanation
Indices: 4644471--4644515 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
4644461 TTATTATTAT
4644471 TTATTTAGTTTTA
1 TTATTTAGTTTTA
*
4644484 TTATTTATTTTTA
1 TTATTTAGTTTTA
4644497 -T-TTTA-TTTTA
1 TTATTTAGTTTTA
4644507 TTAATTTAG
1 TT-ATTTAG
4644516 GATTAAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 1 0.04
13 16 0.59
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:4644496 original size:23 final size:24
Alignment explanation
Indices: 4644464--4644514 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
4644454 GAAGATATTA
4644464 TTATTATTTA-TTTAGTTTTATTAT
1 TTATTATTTATTTTA-TTTTATTAT
4644488 TTATT-TTTATTTTATTTTATTAAT
1 TTATTATTTATTTTATTTTATT-AT
4644512 TTA
1 TTA
4644515 GGATTAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTATTATTTATTTTATTTTATTAT
Found at i:4647310 original size:31 final size:31
Alignment explanation
Indices: 4647273--4647338 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
4647263 ACTGGGTGTG
*
4647273 TGGGCCCACATGAGTAGTCCACACGGGCATA
1 TGGGCCCACATGAGTAGTCCAAACGGGCATA
* * *
4647304 TGGGCCCACATGGGTAGTCCAAACTGGTATA
1 TGGGCCCACATGAGTAGTCCAAACGGGCATA
4647335 TGGG
1 TGGG
4647339 TTGCTGGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (31 bp):
TGGGCCCACATGAGTAGTCCAAACGGGCATA
Found at i:4650674 original size:16 final size:16
Alignment explanation
Indices: 4650652--4650685 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4650642 AACTAAAACT
4650652 TTAT-TTTTAATTTT-
1 TTATATTTTAATTTTA
4650666 TTATATTTTAATTTTA
1 TTATATTTTAATTTTA
4650682 TTAT
1 TTAT
4650686 GCATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 10 0.56
16 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATATTTTAATTTTA
Found at i:4653499 original size:32 final size:31
Alignment explanation
Indices: 4653463--4653522 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4653453 AAATTAGTAA
4653463 ATTTAATCTTCCTTAAAAATAATAAAAATTTT
1 ATTTAAT-TTCCTTAAAAATAATAAAAATTTT
** *
4653495 ATTTAATTTTTTTAAAAATTATAAAAAT
1 ATTTAATTTCCTTAAAAATAATAAAAAT
4653523 ATAAACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTTAATTTCCTTAAAAATAATAAAAATTTT
Found at i:4655249 original size:3 final size:3
Alignment explanation
Indices: 4655236--4655277 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
4655226 ACAAACAATG
* *
4655236 ATA AAA ATA ATA ATA AAA ATA ATA ATA ATTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT
4655278 GTAATGATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:4655253 original size:12 final size:12
Alignment explanation
Indices: 4655236--4655276 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
4655226 ACAAACAATG
4655236 ATAAAAATAATA
1 ATAAAAATAATA
4655248 ATAAAAATAATA
1 ATAAAAATAATA
*
4655260 ATAATTAATAATA
1 ATAA-AAATAATA
4655273 ATAA
1 ATAA
4655277 TGTAATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:4655833 original size:13 final size:13
Alignment explanation
Indices: 4655787--4655833 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
4655777 ACAATATATA
4655787 ATATATAAAAAA-
1 ATATATAAAAAAT
4655799 ATATATAAATATAAT
1 ATATATAAA-A-AAT
*
4655814 ATTTATAAAAAAT
1 ATATATAAAAAAT
*
4655827 ACATATA
1 ATATATA
4655834 TGGTATAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.31
13 9 0.31
14 3 0.10
15 8 0.28
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATATAAAAAAT
Found at i:4659665 original size:22 final size:22
Alignment explanation
Indices: 4659630--4659671 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4659620 ATACTTATTT
* *
4659630 TATTTTACATTGATTAGAATTC
1 TATTTGACACTGATTAGAATTC
4659652 TATTTGACACTGATTAGAAT
1 TATTTGACACTGATTAGAAT
4659672 AAGATTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (22 bp):
TATTTGACACTGATTAGAATTC
Found at i:4667922 original size:21 final size:21
Alignment explanation
Indices: 4667896--4667946 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
4667886 CGCTATTTCT
* * *
4667896 AATCTCATCGCTATAGTATCC
1 AATCTCACCACTATAGTAACC
*
4667917 AATCTCACCACTATAGTAACT
1 AATCTCACCACTATAGTAACC
4667938 AATCTCACC
1 AATCTCACC
4667947 GCCACTACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.29
Consensus pattern (21 bp):
AATCTCACCACTATAGTAACC
Found at i:4668960 original size:63 final size:63
Alignment explanation
Indices: 4668874--4669245 Score: 372
Period size: 63 Copynumber: 5.9 Consensus size: 63
4668864 TGCCTTGCCC
* * * * *
4668874 GTGTGTCTCAAATATAAACTCAGTGAGTCACACGGCCTAGACACACGCCCGTGTGTCTTGCCT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * * * * **
4668937 ATATGCCTCTAATACAAACTCAGTGAGTTATACGGCTTGGACACACGCCCGTGTGTCTTGTCT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * ** * *
4669000 ATGTG-CATCTAATATGAACTCAGTGAGTGACACGGCCTGGACACACGCCTATGTGTCTCACCC
1 GTGTGAC-TCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * *
4669063 GTGTGACTCTAATATGAATTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * ** * ** *
4669126 GTATGACTCTAATATGAACTTAGTGAGTTACA-AACCTGGACATACGCTTGTGTGTCTCA-CT
1 GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
* * * * *
4669187 CGTGTGACTCTAATATAAACTCAGTGTGTTACACGGCCTAGATACATGCCCATGTGTCT
1 -GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCT
4669246 CACCCATATG
Statistics
Matches: 256, Mismatches: 49, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
61 2 0.01
62 51 0.20
63 202 0.79
64 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (63 bp):
GTGTGACTCTAATATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTTACCT
Found at i:4669086 original size:126 final size:126
Alignment explanation
Indices: 4668884--4669256 Score: 417
Period size: 126 Copynumber: 3.0 Consensus size: 126
4668874 GTGTGTCTCA
* * * ** ** * *
4668884 AATATAAACTCAGTGAGTCACACGGCCTAGACACACGCCCGTGTGTCTTGCCTATATGCCTCTAA
1 AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
* * * *** *
4668949 TACAAACTCAGTGAGTTATACGGCTTGGACACACGCCCGTGTGTCTTGTCTATGTG-CATCT
66 TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGAC-TCT
* *
4669010 AATATGAACTCAGTGAGTGACACGGCCTGGACACACGCCTATGTGTCTCACCCGTGTGACTCTAA
1 AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
* * *
4669075 TATGAATTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTGTATGACTCT
66 TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGACTCT
* * ** * * *
4669136 AATATGAACTTAGTGAGTTACA-AACCTGGACATACGCTTGTGTGTCTCACTCGTGTGACTCTAA
1 AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
* * * * * *
4669200 TATAAACTCAGTGTGTTACACGGCCTAGATACATGCCCATGTGTCTCACCCATATGA
66 TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGA
4669257 TTCCTGTATC
Statistics
Matches: 208, Mismatches: 38, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
125 84 0.40
126 123 0.59
127 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (126 bp):
AATATGAACTCAGTGAGTCACACGGCCTGGACACACGCCTGTGTGTCTCACCCGTGTGACTCTAA
TATAAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCTCACCTATATGACTCT
Found at i:4677350 original size:25 final size:25
Alignment explanation
Indices: 4677316--4677371 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
4677306 CCCAGATCAG
*
4677316 TTCATAGAAAGATCTAGCACAAGCT
1 TTCATGGAAAGATCTAGCACAAGCT
4677341 TTCATGGAAAGATCTAGCACAAGCT
1 TTCATGGAAAGATCTAGCACAAGCT
4677366 TTCATG
1 TTCATG
4677372 AAGCAGTACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (25 bp):
TTCATGGAAAGATCTAGCACAAGCT
Found at i:4681779 original size:804 final size:804
Alignment explanation
Indices: 4680231--4682642 Score: 4628
Period size: 804 Copynumber: 3.0 Consensus size: 804
4680221 CAGGTCTCCA
*
4680231 GATATCAACGATGTGAGTGACGTTGTTACTAATTCAGAGTCCCCTTTTGAGCGGGATATGTGTCT
1 GATATCAACGATGTGAGTGACGTTGCTACTAATTCAGAGTCCCCTTTTGAGCGGGATATGTGTCT
4680296 AGAGGGATCTCAGGACTTTGAGGATGACGGAGACTGTAACTCATCCCTTGATTTGTTAAGGATGG
66 AGAGGGATCTCAGGACTTTGAGGATGACGGAGACTGTAACTCATCCCTTGATTTGTTAAGGATGG
4680361 TAGAACACGAGGAGAAACAGATTCTACCCCACAAAGAGACCGTAGAAGTCGTGAACTTGGGAGAT
131 TAGAACACGAGGAGAAACAGATTCTACCCCACAAAGAGACCGTAGAAGTCGTGAACTTGGGAGAT
4680426 GAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGACCTTAT
196 GAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGACCTTAT
4680491 TGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGCTAAGTA
261 TGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGCTAAGTA
*
4680556 CTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATAGAAGCCGGTTCAGCAAAAGCTTCGA
326 CTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATGGAAGCCGGTTCAGCAAAAGCTTCGA
*
4680621 AGGATGTGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGCTGGTTT
391 AGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGCTGGTTT
4680686 CTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAGGTGGAA
456 CTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAGGTGGAA
4680751 AAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTCCCGTTG
521 AAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTCCCGTTG
4680816 CCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGATGGTTT
586 CCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGATGGTTT
4680881 CTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGACCATGT
651 CTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGACCATGT
* * *
4680946 GGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATAGAAAAATACGGGAGCAACATATCAGAGA
716 GGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATATCAGAGA
4681011 GCCATGGTAACCCTATTCCATGAT
781 GCCATGGTAACCCTATTCCATGAT
*
4681035 GATATCAACGATGTGAGTGATGTTGCTACTAATTCAGAGTCCCCTTTTGAGCGGGATATGTGTCT
1 GATATCAACGATGTGAGTGACGTTGCTACTAATTCAGAGTCCCCTTTTGAGCGGGATATGTGTCT
4681100 AGAGGGATCTCAGGACTTTGAGGATGACGGAGACTGTAACTCATCCCTTGATTTGTTAAGGATGG
66 AGAGGGATCTCAGGACTTTGAGGATGACGGAGACTGTAACTCATCCCTTGATTTGTTAAGGATGG
*
4681165 TAGAACACGAGGAGAAACAGATTCTACCCCACAAAGTGACCGTAGAAGTCGTGAACTTGGGAGAT
131 TAGAACACGAGGAGAAACAGATTCTACCCCACAAAGAGACCGTAGAAGTCGTGAACTTGGGAGAT
4681230 GAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGACCTTAT
196 GAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGACCTTAT
* *
4681295 TGAGTTACTTCAAGAGTTCAAGGGTGTCTTTGCATGGTCATATCAAGATATGCCTGGGCTAAGTA
261 TGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGCTAAGTA
4681360 CTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATGGAAGCCGGTTCAGCAAAAGCTTCGA
326 CTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATGGAAGCCGGTTCAGCAAAAGCTTCGA
4681425 AGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGCTGGTTT
391 AGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGCTGGTTT
*
4681490 CTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCCTCCCCGTCCCTAAAAAAGGTGGAA
456 CTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAGGTGGAA
4681555 AAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTCCCGTTG
521 AAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTCCCGTTG
4681620 CCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGATGGTTT
586 CCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGATGGTTT
4681685 CTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGACCATGT
651 CTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGACCATGT
*
4681750 GGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGTAATATATCAGAGA
716 GGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATATCAGAGA
*
4681815 TCCATGGTAACCCTATTCCATGAT
781 GCCATGGTAACCCTATTCCATGAT
*
4681839 GATATCAACGATGTGAGTGACGTTGCTACTTATTCAGAGTCCCCTTTTGAGCGGGATATGTGTCT
1 GATATCAACGATGTGAGTGACGTTGCTACTAATTCAGAGTCCCCTTTTGAGCGGGATATGTGTCT
*
4681904 AGAGGGATCTCAGGACTTTGAGGATGACGGAGACTGTAACTCATCCCTTGATTTGTTAATGATGG
66 AGAGGGATCTCAGGACTTTGAGGATGACGGAGACTGTAACTCATCCCTTGATTTGTTAAGGATGG
* *
4681969 TAGAACACGAGGAGAAACAGATTCTACCCTATAAAGAGACCGTAGAAGTCGTGAACTTGGGAGAT
131 TAGAACACGAGGAGAAACAGATTCTACCCCACAAAGAGACCGTAGAAGTCGTGAACTTGGGAGAT
4682034 GAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGACCTTAT
196 GAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGACCTTAT
4682099 TGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGCTAAGTA
261 TGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGCTAAGTA
*
4682164 CTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATGGAAGCCGGTTCAACAAAAGCTTCGA
326 CTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATGGAAGCCGGTTCAGCAAAAGCTTCGA
4682229 AGGATGC-GCCCTGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGCTGGTT
391 AGGATGCGGCCC-GATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGCTGGTT
4682293 TCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAGGTGGA
455 TCTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAGGTGGA
* *
4682358 AAAGTACGGATGTGTGTAGACTAAATAGACTTAAACAAAGCCAGCCCGAAGGATAATTTCCCGTT
520 AAAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTCCCGTT
4682423 GCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGATGGTT
585 GCCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGATGGTT
4682488 TCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGACCATG
650 TCTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGACCATG
4682553 TGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATATCAGAG
715 TGGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATATCAGAG
4682618 AGCCATGGTAACCCTATTCCATGAT
780 AGCCATGGTAACCCTATTCCATGAT
4682643 ATGATGCATA
Statistics
Matches: 1580, Mismatches: 27, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
803 4 0.00
804 1576 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (804 bp):
GATATCAACGATGTGAGTGACGTTGCTACTAATTCAGAGTCCCCTTTTGAGCGGGATATGTGTCT
AGAGGGATCTCAGGACTTTGAGGATGACGGAGACTGTAACTCATCCCTTGATTTGTTAAGGATGG
TAGAACACGAGGAGAAACAGATTCTACCCCACAAAGAGACCGTAGAAGTCGTGAACTTGGGAGAT
GAACTAGAAAAGAAAGAAGTAAATATCGGAGCTTGTATTACCACAGAGACAAAGCGGGACCTTAT
TGAGTTACTCCAAGAGTTCAAGGATGTCTTTGCATGGTCATATCAAGATATGCCTGGGCTAAGTA
CTGACATTGTGGTACACAGGCTCCCCATCAAAGAAGAATGGAAGCCGGTTCAGCAAAAGCTTCGA
AGGATGCGGCCCGATGTTTTGTTGAAAATAAAAGAGGAGGTCAAGAAGCAATTTGATGCTGGTTT
CTTATAAGTAGTTAAGTACTCAGAATGGGTAACCAACATCATCCCCGTCCCTAAAAAAGGTGGAA
AAGTACGGATGTGTGTAGACTACAGAGACTTAAACAAAGCCAGCCCGAAGGATAATTTCCCGTTG
CCTCATATTGACACCTTAGTGGATAACACGGCAGGTTACTCACTCTTCTCCTTCATGGATGGTTT
CTCAGGGTACAATTAGATCAAGATGCATCCTGAAGACATGAATAAAACCACATTTGTGACCATGT
GGGGAGCCTTTTGCTATAAGGTGATGCCGTTCGGATTGAAAAATGCGGGAGCAATATATCAGAGA
GCCATGGTAACCCTATTCCATGAT
Found at i:4686281 original size:44 final size:44
Alignment explanation
Indices: 4686210--4686719 Score: 270
Period size: 44 Copynumber: 11.6 Consensus size: 44
4686200 ATTCAGAAGC
*
4686210 CTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
* * * * * * *** *
4686254 CTTATCTCCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATGGGCT
1 CTTAACCCCCTAAGCAGTAGGGTAACAG-GCTAA-ATTTACAAGAT
* ** *
4686299 -TTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTAC-AGAC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
* *
4686341 CTTAAACCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
* * * * * * *** *
4686385 CTTATCTCCCTAAGCAGTAGGGAAACAGATCGAACA-TGATGGGCT
1 CTTAACCCCCTAAGCAGTAGGGTAACAG-GCTAA-ATTTACAAGAT
* * *
4686430 -TTAACCCCCTAAGCAGTAGGGTAACAGGTTGAGTTTAC-AGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
* * * ** * * *
4686472 TTTAACCCCCTAAGCAGTAGGGAAACA-GATCAAA-GAAGATGAGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAATTTACAAGA-T
4686516 CTTGAA-CCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
1 CTT-AACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
* * * *** *
4686560 CTTATCTCCCTAAACAGTAGGGTAACAGGCTGAAGAGCGACGAG-T
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AA-ATTTACAAGAT
* * ** * ** * *** *
4686605 CTTAACCCCTTAAGCAGTAGGGAAACAAATCGAAGGTGATGGGCT
1 CTTAACCCCCTAAGCAGTAGGGTAAC-AGGCTAAATTTACAAGAT
* * * *
4686650 -TTAACCCCCTAAGTAGTAGGGTAACAAGCTGAATTTGC-AGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
* * *
4686692 CTTAAACCCCTAAGTAGTAGGGAAACAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAG
4686720 ATCAAAGAAG
Statistics
Matches: 340, Mismatches: 105, Indels: 43
0.70 0.22 0.09
Matches are distributed among these distances:
42 9 0.03
43 98 0.29
44 175 0.51
45 49 0.14
46 9 0.03
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (44 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT
Found at i:4686399 original size:87 final size:87
Alignment explanation
Indices: 4686305--4686587 Score: 311
Period size: 87 Copynumber: 3.2 Consensus size: 87
4686295 GGCTTTAACC
* * * * *
4686305 CCCTAAGCAGTAGGGTAACA-AGCCGAATTTACAGACCTTAAACCCCTAAGTAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAGA-TCGAAATAACAGACCTTAAACCCCTAAGCAGTAGGGTAACAG
4686369 GCTAAATTTACAAGATCTTATCT
65 GCTAAATTTACAAGATCTTATCT
* ** * * *
4686392 CCCTAAGCAGTAGGGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAGATCGAA-ATAACAGACCTTAAACCCCTAAGCAGTAGGGTAACAG
* * * * * *
4686457 GTTGAGTTTAC-AGATTTTAACC
65 GCTAAATTTACAAGATCTTATCT
* * *
4686479 CCCTAAGCAGTAGGGAAACAGATC-AAAGAAGATGAGCCTTGAACCCCTAAGCAGTAGGGTAACA
1 CCCTAAGCAGTAGGGAAACAGATCGAAATAACA-GA-CCTTAAACCCCTAAGCAGTAGGGTAACA
4686543 GGCTAAATTTACAAGATCTTATCT
64 GGCTAAATTTACAAGATCTTATCT
* *
4686567 CCCTAAACAGTAGGGTAACAG
1 CCCTAAGCAGTAGGGAAACAG
4686588 GCTGAAGAGC
Statistics
Matches: 159, Mismatches: 32, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
85 2 0.01
86 3 0.02
87 89 0.56
88 65 0.41
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (87 bp):
CCCTAAGCAGTAGGGAAACAGATCGAAATAACAGACCTTAAACCCCTAAGCAGTAGGGTAACAGG
CTAAATTTACAAGATCTTATCT
Found at i:4686432 original size:131 final size:131
Alignment explanation
Indices: 4686209--4686499 Score: 492
Period size: 131 Copynumber: 2.2 Consensus size: 131
4686199 AATTCAGAAG
4686209 CCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGATCTTATCTCCCTAAGCAGTAG
1 CCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGATCTTATCTCCCTAAGCAGTAG
*
4686274 GGAAACAGATCGAAGATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
66 GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
4686339 A
131 A
*
4686340 CCTTAAACCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGATCTTATCTCCCTAAGCAGTAG
1 CCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGATCTTATCTCCCTAAGCAGTAG
* ** *
4686405 GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAGGTTGAGTTTACAG
66 GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
4686470 A
131 A
** * *
4686471 TTTTAACCCCCTAAGCAGTAGGGAAACAG
1 CCTTAACCCCCTAAGTAGTAGGGTAACAG
4686500 ATCAAAGAAG
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 149 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (131 bp):
CCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGATCTTATCTCCCTAAGCAGTAG
GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
A
Found at i:4686527 original size:131 final size:131
Alignment explanation
Indices: 4686209--4686543 Score: 397
Period size: 131 Copynumber: 2.6 Consensus size: 131
4686199 AATTCAGAAG
* * * ** * *
4686209 CCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGATCTTATCTCCCTAAGCAGTAG
1 CCTTAAACCCCTAAGCAGTAGGGAAACAGGCTAAATGAACAAGACCTTAACTCCCTAAGCAGTAG
*
4686274 GGAAACAGATCGAAGATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
66 GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
4686339 A
131 A
* * ** * *
4686340 CCTTAAACCCCTAAGTAGTAGGGTAACAGGCTAAATTTACAAGATCTTATCTCCCTAAGCAGTAG
1 CCTTAAACCCCTAAGCAGTAGGGAAACAGGCTAAATGAACAAGACCTTAACTCCCTAAGCAGTAG
* ** *
4686405 GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAGGTTGAGTTTACAG
66 GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
4686470 A
131 A
** * * * *
4686471 TTTTAACCCCCTAAGCAGTAGGGAAACA-GATCAAA-GAAGATGAGCCTTGAAC-CCCTAAGCAG
1 CCTTAAACCCCTAAGCAGTAGGGAAACAGGCT-AAATGAACAAGA-CCTT-AACTCCCTAAGCAG
*
4686533 TAGGGTAACAG
63 TAGGGAAACAG
4686544 GCTAAATTTA
Statistics
Matches: 182, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
130 6 0.03
131 174 0.96
132 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (131 bp):
CCTTAAACCCCTAAGCAGTAGGGAAACAGGCTAAATGAACAAGACCTTAACTCCCTAAGCAGTAG
GGAAACAGATCGAACATGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAG
A
Found at i:4686734 original size:87 final size:87
Alignment explanation
Indices: 4686567--4686762 Score: 225
Period size: 87 Copynumber: 2.2 Consensus size: 87
4686557 GATCTTATCT
* * **
4686567 CCCTAAACAGTAGGGTAACAGGCTGAA-GAGCGACGAGTCTTAACCCCTTAAGCAGTAGGGAAAC
1 CCCTAAGCAGTAGGGTAACAAGCTGAATTTGC-A-GA-TCTTAACCCCTTAAGCAGTAGGGAAAC
* ** *
4686631 AAATCGAAGGTGATGGGCTTTAACC
63 AAATCAAAGAAGATGGGCCTTAACC
* * *
4686656 CCCTAAGTAGTAGGGTAACAAGCTGAATTTGCAGATCTTAAACCCC-TAAGTAGTAGGGAAACAG
1 CCCTAAGCAGTAGGGTAACAAGCTGAATTTGCAGATCTT-AACCCCTTAAGCAGTAGGGAAACAA
4686720 ATCAAAGAAGATGGGCCTTAACC
65 ATCAAAGAAGATGGGCCTTAACC
**
4686743 CTTTAAGCAGTAGGGTAACA
1 CCCTAAGCAGTAGGGTAACA
4686763 GGCTAAAAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
87 56 0.62
88 8 0.09
89 25 0.27
90 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (87 bp):
CCCTAAGCAGTAGGGTAACAAGCTGAATTTGCAGATCTTAACCCCTTAAGCAGTAGGGAAACAAA
TCAAAGAAGATGGGCCTTAACC
Found at i:4686743 original size:43 final size:43
Alignment explanation
Indices: 4686392--4686763 Score: 125
Period size: 44 Copynumber: 8.5 Consensus size: 43
4686382 GATCTTATCT
* * * *
4686392 CCCTAAGCAGTAGGGAAACAGATCGAACATGATGGGCTTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCAAAGAAGATGGGCCTTAA-C
* * ** *** ** ***
4686436 CCCTAAGCAGTAGGGTAACAGGT-TGAGTTTACAGATTTTAACC
1 CCCTAAGCAGTAGGGAAACAGATCAAAGAAGATGGGCCTTAA-C
*
4686479 CCCTAAGCAGTAGGGAAACAGATCAAAGAAGATGAGCCTTGAAC
1 CCCTAAGCAGTAGGGAAACAGATCAAAGAAGATGGGCCTT-AAC
* * * * *
4686523 CCCTAAGCAGTAGGGTAACAGGCTAAATTTACAAGAT----CTTATC
1 CCCTAAGCAGTAGGGAAACA-GATCAA---AGAAGATGGGCCTTAAC
* * * * * * * *
4686566 TCCCTAAACAGTAGGGTAACAG-GCTGAAGAGCGACGAGTCTTAAC
1 -CCCTAAGCAGTAGGGAAACAGATC-AAAGA-AGATGGGCCTTAAC
* * ** *
4686611 CCCTTAAGCAGTAGGGAAACAAATCGAAGGTGATGGGCTTTAACC
1 CCC-TAAGCAGTAGGGAAACAGATCAAAGAAGATGGGCCTTAA-C
* * * * * *
4686656 CCCTAAGTAGTAGGGTAACAAGCTGAATTTGCAGAT----CTTAAAC
1 CCCTAAGCAGTAGGGAAAC-AGATCAA--AGAAGATGGGCCTT-AAC
*
4686699 CCCTAAGTAGTAGGGAAACAGATCAAAGAAGATGGGCCTTAAC
1 CCCTAAGCAGTAGGGAAACAGATCAAAGAAGATGGGCCTTAAC
* *
4686742 CCTTTAAGCAGTAGGGTAACAG
1 CC-CTAAGCAGTAGGGAAACAG
4686764 GCTAAAAATC
Statistics
Matches: 238, Mismatches: 65, Indels: 50
0.67 0.18 0.14
Matches are distributed among these distances:
40 7 0.03
41 2 0.01
42 5 0.02
43 62 0.26
44 114 0.48
45 37 0.16
46 1 0.00
47 4 0.02
48 6 0.03
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGAAACAGATCAAAGAAGATGGGCCTTAAC
Found at i:4687163 original size:38 final size:38
Alignment explanation
Indices: 4687121--4687194 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
4687111 TTCATTCAGT
4687121 CCATTTTACAACTTTTGACCCAAACACAAAACCCAAAC
1 CCATTTTACAACTTTTGACCCAAACACAAAACCCAAAC
4687159 CCATTTTACAACTTTTGACCCAAACACAAAACCCAA
1 CCATTTTACAACTTTTGACCCAAACACAAAACCCAA
4687195 TCTGAACCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.42, C:0.34, G:0.03, T:0.22
Consensus pattern (38 bp):
CCATTTTACAACTTTTGACCCAAACACAAAACCCAAAC
Found at i:4690338 original size:12 final size:12
Alignment explanation
Indices: 4690298--4690344 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
4690288 GTGTTATTTT
4690298 TATTATTATTA-
1 TATTATTATTAC
4690309 T-TTATTATTAC
1 TATTATTATTAC
* *
4690320 CACTATTATTAC
1 TATTATTATTAC
*
4690332 TATTATTTTTAC
1 TATTATTATTAC
4690344 T
1 T
4690345 TTTTGCTACC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
10 9 0.31
11 1 0.03
12 19 0.66
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:4690429 original size:12 final size:12
Alignment explanation
Indices: 4690392--4690440 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
4690382 TTTCTTTTAC
*
4690392 TATTGTCATTAT
1 TATTATCATTAT
4690404 TATTAATACTATTAT
1 TATT-AT-C-ATTAT
*
4690419 TATTATCATTAG
1 TATTATCATTAT
4690431 TATTATCATT
1 TATTATCATT
4690441 TTTTGCTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 18 0.56
13 2 0.06
14 3 0.09
15 9 0.28
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (12 bp):
TATTATCATTAT
Found at i:4694104 original size:38 final size:38
Alignment explanation
Indices: 4694042--4694139 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 38
4694032 ATTTGATGTG
4694042 TATCCGGGCTTAAAGAT-CCGCAGGCTAT-ATGCTAGAATTA
1 TATCCGGG-TT-AA-ATCCCGCAGGCT-TCATGCTAGAATTA
* * *
4694082 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTAGAATTA
*
4694120 TATCAGGGTTAAATCCCGCA
1 TATCCGGGTTAAATCCCGCA
4694140 AGCCTAGTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
37 3 0.06
38 39 0.75
39 2 0.04
40 8 0.15
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCATGCTAGAATTA
Found at i:4694150 original size:38 final size:38
Alignment explanation
Indices: 4694078--4694161 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
4694068 ATATGCTAGA
* * * *
4694078 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
1 ATTATATCAGGGTTAAATCCCGCAAGCCTAGTGCTGGT
4694116 ATTATATCAGGGTTAAATCCCGCAAGCCTAGTGCTGGT
1 ATTATATCAGGGTTAAATCCCGCAAGCCTAGTGCTGGT
4694154 ATTATATC
1 ATTATATC
4694162 TAAGTTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (38 bp):
ATTATATCAGGGTTAAATCCCGCAAGCCTAGTGCTGGT
Found at i:4695859 original size:43 final size:43
Alignment explanation
Indices: 4695743--4695920 Score: 286
Period size: 43 Copynumber: 4.2 Consensus size: 43
4695733 GCATGAAACT
*
4695743 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGCGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
*
4695786 CGGTGATGTGTA-TCGGGCCTTCGTACCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
*
4695828 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGT
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * **
4695871 CAGTGATGTGTATTCGGGTCTTCGTGCCTAGCAGGCTTAATGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
4695914 CGGTGAT
1 CGGTGAT
4695921 TCGAGCAAGG
Statistics
Matches: 124, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
42 40 0.32
43 84 0.68
ACGTcount: A:0.12, C:0.24, G:0.34, T:0.30
Consensus pattern (43 bp):
CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
Found at i:4696143 original size:58 final size:58
Alignment explanation
Indices: 4696074--4696242 Score: 277
Period size: 58 Copynumber: 2.9 Consensus size: 58
4696064 CGAATGATTA
*
4696074 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
* *
4696132 GAGGCACTGTGTGTGCGAATTCCTTTAACCAAGCACTATGTGTGCGAGATCGATAATT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
* * *
4696190 GAGGCATTGTGTGTGCGAGTT-CTTCAACCGAGCACTATGTGTGCGAGATCGGT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGT
4696243 CAGTGGGCAC
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
57 29 0.28
58 74 0.72
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (58 bp):
GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
Found at i:4696177 original size:29 final size:29
Alignment explanation
Indices: 4696077--4696178 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
4696067 ATGATTAGAG
* * *
4696077 GCACTGTGTGTGCAAATTCCTTTAACCGA
1 GCACTATGTGTGCGAATTCCTTTAACCAA
** ** *
4696106 GCACTATGTGTGCGAGA-T-CGGTAATTGAG
1 GCACTATGTGTGCGA-ATTCCTTTAA-CCAA
*
4696135 GCACTGTGTGTGCGAATTCCTTTAACCAA
1 GCACTATGTGTGCGAATTCCTTTAACCAA
4696164 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
4696179 GATCGATAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
28 5 0.09
29 44 0.81
30 5 0.09
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (29 bp):
GCACTATGTGTGCGAATTCCTTTAACCAA
Found at i:4696202 original size:29 final size:29
Alignment explanation
Indices: 4696106--4696208 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 29
4696096 CTTTAACCGA
* *
4696106 GCACTATGTGTGCGAGATCGGTAATTGAG
1 GCACTGTGTGTGCGAGATCGATAATTGAG
** ** *
4696135 GCACTGTGTGTGCGA-ATTCCTTTAA-CCAA
1 GCACTGTGTGTGCGAGA-T-CGATAATTGAG
*
4696164 GCACTATGTGTGCGAGATCGATAATTGAG
1 GCACTGTGTGTGCGAGATCGATAATTGAG
*
4696193 GCATTGTGTGTGCGAG
1 GCACTGTGTGTGCGAG
4696209 TTCTTCAACC
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
28 5 0.09
29 46 0.82
30 5 0.09
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
GCACTGTGTGTGCGAGATCGATAATTGAG
Found at i:4699865 original size:38 final size:38
Alignment explanation
Indices: 4699803--4699903 Score: 116
Period size: 38 Copynumber: 2.6 Consensus size: 38
4699793 ATTTGATGTG
4699803 TATCCGGGCTTAAAGAT-CCGCAGGCTAT-ATGCTAGAATTA
1 TATCCGGG-TT-AA-ATCCCGCAGGCT-TCATGCTAGAATTA
* * *
4699843 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCATGCTAGAATTA
*
4699881 TATCAGGGTTAAATCCCGCAGGC
1 TATCCGGGTTAAATCCCGCAGGC
4699904 CTAGTGCTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
37 3 0.05
38 42 0.76
39 2 0.04
40 8 0.15
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCATGCTAGAATTA
Found at i:4699911 original size:38 final size:38
Alignment explanation
Indices: 4699839--4699922 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 38
4699829 ATATGCTAGA
* * *
4699839 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
1 ATTATATCAGGGTTAAATCCCGCAGGCCTAGTGCTGGT
4699877 ATTATATCAGGGTTAAATCCCGCAGGCCTAGTGCTGGT
1 ATTATATCAGGGTTAAATCCCGCAGGCCTAGTGCTGGT
4699915 ATTATATC
1 ATTATATC
4699923 TAAGTTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (38 bp):
ATTATATCAGGGTTAAATCCCGCAGGCCTAGTGCTGGT
Found at i:4702179 original size:13 final size:13
Alignment explanation
Indices: 4702155--4702193 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
4702145 ATTAGATTAA
4702155 ATTATA-TATTTT
1 ATTATATTATTTT
4702167 ATTATATTATTTT
1 ATTATATTATTTT
*
4702180 AATATATTAATTTT
1 ATTATATT-ATTTT
4702194 TGTTATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.25
13 13 0.54
14 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTATATTATTTT
Found at i:4703257 original size:59 final size:59
Alignment explanation
Indices: 4703184--4703302 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
4703174 TATGAATAAT
*
4703184 AATCAAATTTATACAAATGTAAATTTGTTATTTTATTTCTCAAGTTTCTATTATAAAAA
1 AATCAAATTCATACAAATGTAAATTTGTTATTTTATTTCTCAAGTTTCTATTATAAAAA
4703243 AATCAAATTCATACAAATGTAAATTTGTTATTTTATTTCTCAAGTTTCTATTATAAAAA
1 AATCAAATTCATACAAATGTAAATTTGTTATTTTATTTCTCAAGTTTCTATTATAAAAA
4703302 A
1 A
4703303 TTAACTATCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (59 bp):
AATCAAATTCATACAAATGTAAATTTGTTATTTTATTTCTCAAGTTTCTATTATAAAAA
Found at i:4705588 original size:15 final size:14
Alignment explanation
Indices: 4705568--4705597 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4705558 AAATCTGGTG
4705568 GTGTTGTTGTGTAGA
1 GTGTTGTTG-GTAGA
4705583 GTGTTGTTGGTAGA
1 GTGTTGTTGGTAGA
4705597 G
1 G
4705598 CTTTTCCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.43
Consensus pattern (14 bp):
GTGTTGTTGGTAGA
Found at i:4715068 original size:3 final size:3
Alignment explanation
Indices: 4715060--4715093 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
4715050 GTATGTCCAT
*
4715060 TTC TTC TTC TTC TTC TTC TTC TTC AT- TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
4715094 TTTTGCTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4718246 original size:28 final size:28
Alignment explanation
Indices: 4718189--4718251 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
4718179 AAAATTTAAA
*
4718189 AAAAATATTTTTTTAAAATTTTATATTTTT
1 AAAAATA--TTTTTAAAATTTTATAATTTT
* *
4718219 TAAAATATTTTTAATGATTTT-TAATTTT
1 AAAAATATTTTTAA-AATTTTATAATTTT
4718247 AAAAA
1 AAAAA
4718252 ACTAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 17 0.61
29 5 0.18
30 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
AAAAATATTTTTAAAATTTTATAATTTT
Found at i:4718558 original size:16 final size:16
Alignment explanation
Indices: 4718519--4718563 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
4718509 AATATTATAA
* *
4718519 TAATCTTTTTATTAGT
1 TAATCTTTTTATAAAT
*
4718535 T-ATTTTTTTATAAAT
1 TAATCTTTTTATAAAT
4718550 TAATCTTTTTATAA
1 TAATCTTTTTATAA
4718564 TATCATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (16 bp):
TAATCTTTTTATAAAT
Found at i:4728769 original size:11 final size:11
Alignment explanation
Indices: 4728753--4728783 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4728743 TGAAGGAAAA
*
4728753 GACCATGGTTG
1 GACCATGGCTG
4728764 GACCATGGCTG
1 GACCATGGCTG
4728775 GACCATGGC
1 GACCATGGC
4728784 AACAAGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.19
Consensus pattern (11 bp):
GACCATGGCTG
Done.